diff --git a/platform/platform-tests/testSrc/com/intellij/workspaceModel/core/fileIndex/AutoExcludeWorkspaceFileIndexContributorTest.kt b/platform/platform-tests/testSrc/com/intellij/workspaceModel/core/fileIndex/AutoExcludeWorkspaceFileIndexContributorTest.kt
index 7d5c5139cf0d..b1865ac57c6f 100644
--- a/platform/platform-tests/testSrc/com/intellij/workspaceModel/core/fileIndex/AutoExcludeWorkspaceFileIndexContributorTest.kt
+++ b/platform/platform-tests/testSrc/com/intellij/workspaceModel/core/fileIndex/AutoExcludeWorkspaceFileIndexContributorTest.kt
@@ -3,10 +3,14 @@ package com.intellij.workspaceModel.core.fileIndex
 
 import com.intellij.openapi.application.readAction
 import com.intellij.openapi.vfs.VirtualFile
+import com.intellij.platform.backend.workspace.workspaceModel
+import com.intellij.platform.workspace.jps.entities.ModuleEntity
+import com.intellij.platform.workspace.jps.entities.modifyModuleEntity
 import com.intellij.testFramework.PsiTestUtil
 import com.intellij.testFramework.junit5.RegistryKey
 import com.intellij.testFramework.junit5.TestApplication
 import com.intellij.testFramework.rules.ProjectModelExtension
+import com.intellij.workspaceModel.ide.legacyBridge.impl.java.JAVA_MODULE_ENTITY_TYPE_ID
 import com.intellij.workspaceModel.ide.registerProjectRoot
 import kotlinx.coroutines.runBlocking
 import org.junit.jupiter.api.Assertions.assertFalse
@@ -34,6 +38,11 @@ class AutoExcludeWorkspaceFileIndexContributorTest {
 
   @Test
   fun `default excluded directories are not in content after project root entity is added`() = runBlocking {
+    projectModel.project.workspaceModel.update("convert module to java") {
+      it.modifyModuleEntity(it.entities(ModuleEntity::class.java).first()) {
+        type = JAVA_MODULE_ENTITY_TYPE_ID
+      }
+    }
     val worktreesDir = projectModel.baseProjectDir.newVirtualDirectory("projectRoot/.worktrees")
     val claudeWorktreesDir = projectModel.baseProjectDir.newVirtualDirectory("projectRoot/.claude/worktrees")
     val srcDir = projectModel.baseProjectDir.newVirtualDirectory("projectRoot/src")
@@ -48,6 +57,24 @@ class AutoExcludeWorkspaceFileIndexContributorTest {
     assertTrue(readAction { fileIndex.isInContent(srcDir) })
   }
 
+  @Test
+  fun `default excluded directories are not in content after non-java module is added`() = runBlocking {
+    val moduleRoot = projectModel.baseProjectDir.newVirtualDirectory("moduleRoot")
+    val worktreesDir = projectModel.baseProjectDir.newVirtualDirectory("moduleRoot/.worktrees")
+    val claudeWorktreesDir = projectModel.baseProjectDir.newVirtualDirectory("moduleRoot/.claude/worktrees")
+    val srcDir = projectModel.baseProjectDir.newVirtualDirectory("moduleRoot/src")
+
+    assertFalse(readAction { fileIndex.isInContent(worktreesDir) })
+    assertFalse(readAction { fileIndex.isInContent(srcDir) })
+
+    val module = projectModel.createModule("nonJavaModule")
+    PsiTestUtil.addSourceContentToRoots(module, moduleRoot)
+
+    assertFalse(readAction { fileIndex.isInContent(worktreesDir) })
+    assertFalse(readAction { fileIndex.isInContent(claudeWorktreesDir) })
+    assertTrue(readAction { fileIndex.isInContent(srcDir) })
+  }
+
   @Test
   @RegistryKey(key = "ide.workspace.model.relative.paths.to.exclude.automatically", value = "custom-dir")
   fun `custom registry value specifies which directories to exclude`() = runBlocking {
diff --git a/platform/projectModel-impl/resources/META-INF/WorkspaceModelImpl.xml b/platform/projectModel-impl/resources/META-INF/WorkspaceModelImpl.xml
index c69d7aa1fb6d..8915328b85b9 100644
--- a/platform/projectModel-impl/resources/META-INF/WorkspaceModelImpl.xml
+++ b/platform/projectModel-impl/resources/META-INF/WorkspaceModelImpl.xml
@@ -15,6 +15,7 @@
     <backgroundPostStartupActivity implementation="com.intellij.workspaceModel.ide.impl.VirtualFileUrlsLazyInitializer"/>
     <workspaceModel.fileIndexContributor implementation="com.intellij.workspaceModel.ide.ProjectRootEntityWorkspaceFileIndexContributor"/>
     <workspaceModel.fileIndexContributor implementation="com.intellij.workspaceModel.ide.AutoExcludeWorkspaceFileIndexContributor"/>
+    <workspaceModel.fileIndexContributor implementation="com.intellij.workspaceModel.ide.AutoExcludeInContentRootsWorkspaceFileIndexContributor"/>
   </extensions>
   <applicationListeners>
     <listener class="com.intellij.workspaceModel.ide.impl.GlobalWorkspaceModelSeparationListener"
diff --git a/platform/projectModel-impl/src/com/intellij/workspaceModel/ide/AutoExcludeWorkspaceFileIndexContributor.kt b/platform/projectModel-impl/src/com/intellij/workspaceModel/ide/AutoExcludeWorkspaceFileIndexContributor.kt
index a5d50e2965b6..410dc22d7de8 100644
--- a/platform/projectModel-impl/src/com/intellij/workspaceModel/ide/AutoExcludeWorkspaceFileIndexContributor.kt
+++ b/platform/projectModel-impl/src/com/intellij/workspaceModel/ide/AutoExcludeWorkspaceFileIndexContributor.kt
@@ -2,7 +2,10 @@
 package com.intellij.workspaceModel.ide
 
 import com.intellij.openapi.util.registry.Registry
+import com.intellij.platform.workspace.jps.entities.ContentRootEntity
+import com.intellij.platform.workspace.jps.entities.ModuleEntity
 import com.intellij.platform.workspace.storage.EntityStorage
+import com.intellij.workspaceModel.core.fileIndex.DependencyDescription
 import com.intellij.workspaceModel.core.fileIndex.WorkspaceFileIndexContributor
 import com.intellij.workspaceModel.core.fileIndex.WorkspaceFileSetRegistrar
 
@@ -22,3 +25,23 @@ internal class AutoExcludeWorkspaceFileIndexContributor : WorkspaceFileIndexCont
     }
   }
 }
+
+
+internal class AutoExcludeInContentRootsWorkspaceFileIndexContributor : WorkspaceFileIndexContributor<ContentRootEntity> {
+  override val entityClass: Class<ContentRootEntity>
+    get() = ContentRootEntity::class.java
+
+  override val dependenciesOnOtherEntities: List<DependencyDescription<ContentRootEntity>>
+    get() = listOf(DependencyDescription.OnParent(ModuleEntity::class.java) { it.contentRoots.asSequence() })
+
+  override fun registerFileSets(entity: ContentRootEntity, registrar: WorkspaceFileSetRegistrar, storage: EntityStorage) {
+    val directories = Registry.get("ide.workspace.model.relative.paths.to.exclude.automatically").asString()
+      .split(";").map { it.trim() }.filter { it.isNotEmpty() && it != "." }
+
+    if (entity.module.type?.name != "JAVA_MODULE") { // There can be too many java modules in a project. Also, java projects should be covered by ProjectRootEntity
+      for (dir in directories) {
+        registrar.registerExcludedRoot(entity.url.append(dir), entity)
+      }
+    }
+  }
+}
\ No newline at end of file